Cited by 802Medical Image Segmentation TechniquesAdvanced Neural Network ApplicationsDomain Adaptation and Few-Shot Learning

Segment anything model for medical image analysis: An experimental study

Open access
Mazurowski, Maciej A., Dong, Haoyu, Gu, Hanxue, Yang, Jichen, Konz, Nicholas, Zhang, Yixin·2023·Medical Image Analysis

Abstract

Training segmentation models for medical images continues to be challenging due to the limited availability of data annotations. Segment Anything Model (SAM) is a foundation model trained on over 1 billion annotations, predominantly for natural images, that is intended to segment user-defined objects of interest in an interactive manner. While the model performance on natural images is impressive, medical image domains pose their own set of challenges. Here, we perform an extensive evaluation of SAM’s ability to segment medical images on a collection of 19 medical imaging datasets from various modalities and anatomies. In our experiments, we generated point and box prompts for SAM using a standard method that simulates interactive segmentation. We report the following findings: (1) SAM’s performance based on single prompts highly varies depending on the dataset and the task, from IoU=0.1135 for spine MRI to IoU=0.8650 for hip X-ray. (2) Segmentation performance appears to be better for well-circumscribed objects with prompts with less ambiguity such as the segmentation of organs in computed tomography and poorer in various other scenarios such as the segmentation of brain tumors. (3) SAM performs notably better with box prompts than with point prompts. (4) SAM outperforms similar methods RITM, SimpleClick, and FocalClick in almost all single-point prompt settings. (5) When multiple-point prompts are provided iteratively, SAM’s performance generally improves only slightly while other methods’ performance improves to the level that surpasses SAM’s point-based performance. We also provide several illustrations for SAM’s performance on all tested datasets, iterative segmentation, and SAM’s behavior given prompt ambiguity. We conclude that SAM shows impressive zero-shot segmentation performance for certain medical imaging datasets, but moderate to poor performance for others. SAM has the potential to make a significant impact in automated medical image segmentation in medical imaging, but appropriate care needs to be applied when using it. Code for evaluation SAM is made publicly available at https://github.com/mazurowski-lab/segment-anything-medical-evaluation.

AI snapshot

Written from the paper’s full text.

TL;DR

This experimental study evaluates the Segment Anything Model (SAM) for zero-shot medical image segmentation across 19 public datasets and 28 tasks. SAM shows highly variable performance, performs best with box prompts, and beats RITM/SimpleClick/FocalClick in most single-point settings, but gains little from iterative point prompts and remains moderate-to-poor on many medical tasks.

Key findings

  • SAM’s single-prompt performance varied widely by dataset/task, from IoU=0.1135 for spine MRI to IoU=0.8650 for hip X-ray in the abstract; the Results section reports a range from IoU=0.1136 to IoU=0.9118.
  • Box prompts were clearly superior to point prompts. Mode 4 (one box per object part) had the best average performance at IoU=0.6542; Mode 3 (single box around the entire object) averaged IoU=0.5891.
  • SAM outperformed RITM, SimpleClick, and FocalClick on 24 of 28 tasks with a single non-iterative point prompt, and on 26 of 28 in oracle mode. Average IoU was 0.4595 for SAM, 0.5137 for SAM oracle, 0.2240 for FocalClick, 0.1910 for SimpleClick, and 0.1322 for RITM.
  • With iterative point prompts, SAM improved only slightly and was surpassed by SimpleClick and RITM when five or more points were provided. The correlation between average object size and SAM performance was small and non-statistically significant.

Methods

  • The authors curated 19 publicly available radiological medical imaging datasets covering X-ray, MRI, CT, ultrasound, and PET, yielding 28 segmentation tasks; for 3D modalities, 2D slices were used as inputs.
  • They evaluated five non-iterative prompting modes using points or boxes, iterative point prompting guided by an error map, “segment everything” mode, and prompt ambiguity/oracle outputs.
  • Performance was measured with IoU against ground-truth masks, using SAM’s highest-confidence mask; SAM was compared with RITM, SimpleClick, and FocalClick.

Limitations

  • The paper states that text-based prompting is not commented on because it remains proof-of-concept, and that “segment everything” mode is not elaborated on. It also states future work should include prompt engineering and extension to 3D segmentation.
  • The text makes evident that the study focuses on radiological images and uses 2D slices for 3D modalities, which may not reflect full 3D medical segmentation performance.
  • The paper states that oracle performance assumes knowledge of the true mask and is biased when there is no additional user interaction after initial prompts; iterative prompting also uses the oracle prediction to guide the next prompt.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1016/j.media.2023.102918

Cites

43 of 43 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

0 of 1 cited sources checked · 0 supported · 0 flagged

  • Findingown data
    § Abstract

    SAM's performance based on single prompts varies highly depending on the dataset and task, from IoU=0.1135 for spine MRI to IoU=0.8650 for hip X-ray.

    “(1) SAM's performance based on single prompts highly varies depending on the dataset and the task, from IoU=0.1135 for spine MRI to IoU=0.8650 for hip X-ray.”
    Quote in the paperSubstantial claim
  • Findingnone given
    § Abstract

    SAM performs notably better with box prompts than with point prompts.

    “(3) SAM performs notably better with box prompts than with point prompts.”
    Quote in the paperSubstantial claim
  • Findingown data

    When used in oracle mode, SAM was better than all other methods for 26 out of 28 tasks.

    “When used in oracle mode, SAM was better than all other methods for 26 out of 28 tasks.”
    Quote in the paperSubstantial claim
  • Findingown data

    Prompts indicating each separate part of the object separately are generally superior to prompts indicating only one part or all parts in one box.

    “Moreover, as expected, prompts where each sep- arate part of the object is indicated separately are generally superior to those where only one part is indicated, or all parts are outlined in one box.”
    Quote in the paperSubstantial claim
  • Findingown data

    SAM's performance varies from near-perfect for well-circumscribed objects with unambiguous prompts to very poor, particularly for objects with ambiguous prompts.

    “This figure illustrates a high variability of SAM's performance ranging from near- perfect for well-circumscribed objects with unambiguous prompts to very poor, particularly for objects with ambigu- ous prompts.”
    Quote in the paperSubstantial claim
  • May combine two claims. 5
  • The quote only partly states this claim. 1
  • Classified as probably not a substantial claim. 2
  • May combine two claims.

    Findingown data

    Segment-everything mode provides mixed usefulness and results are somewhat dependent on the number of prompts.

    “We find that this mode provides mixed usefulness and that the results are somewhat dependent on the number of prompts.”
    Quote in the paperNot a substantial claim
  • May combine two claims. The quote only partly states this claim.

    Findingown data

    SAM obtains very limited benefit from additional point prompts in the iterative setting, except for objects with multiple parts.

    “This is due to the fact that SAM does not appear to draw hardly any benefits from additional information provided through the interactive points after two or three points have been provided.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    Some datasets showed high variability of object size within the dataset itself (e.g., kidneys in ultrasound images) while others showed relative consistency of object size (such as bones in hip X-ray images).

    “Some datasets also showed high variability of object size within the dataset itself (e.g., kidneys in ultrasound images) while others showed relative consistency of object size (such as bones in hip X-ray images).”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Interpretationown data
    § 4. Conclusions and discussion

    Overall, SAM shows promise for use in medical images, as long as suitable prompting strategies are used for the dataset and task of choice.

    “Overall, SAM shows promise for use in medical images, as long as suitable prompting strategies are used for the dataset and task of choice.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductown data

    The correlation analysis uses average object sizes in the image and does not consider variation of object sizes in individual datasets.

    “Note that the correlation analysis looks at average object sizes in the image and does not consider the variation of object sizes in the individual datasets.”
    Quote in the paperNot a substantial claim
  • Classified as probably not a substantial claim.

    Premisecitation
    § 1. Introduction

    SAM has achieved impressive/promising zero-shot segmentation performance on a variety of natural image datasets.

    “The recently developed Segment Anything Model is a foundation model that has achieved promising zero-shot segmentation performance on a variety of natural image datasets [18].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [18] Jang, J., Hwang, D., 2022. M3T: Three-dimensional Medical image classifier using Multi-plane and Multi-slice Transformer. In: Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition. pp. 20718–20729. source

      Not checked in the free run.

6 of 6

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • SAM achieves satisfactory segmentation outcomes primarily on medical targets with distinct boundaries but has substantial limitations on targets with weak boundaries or low contrast.

    “For example, the concurrent studies22,23 conducted a comprehensive assessment of SAM across a diverse array of medical images, underscoring that SAM achieved satisfactory segmentation outcomes primarily on targets characterized by distinct boundaries. However, the model exhibited substantial limitations in segmenting typical medical targets with weak boundaries or low contrast.”

    From Segment anything in medical images (2024) · cites this paper as [22]

    The Abstract and Results §3.1 report better segmentation of well-circumscribed objects and poorer results in other cases, supporting the distinct-boundaries comparison. The paper also identifies prompt ambiguity as an important factor; the passages do not establish low contrast or weak boundaries as the specific cause of its poorer results. (LLM, conf=0.84)

    Experimental — accuracy not yet measured
  • Most previous studies evaluated SAM with limited or even only one type of testing mode/strategy.

    “Most previous studies (Ji et al., 2023a; Mazurowski et al., 2023; Zhou et al., 2023) evaluated SAM with limited or even only one type of testing mode / strategy.”

    From Segment anything model for medical images? (2024) · cites this paper as Mazurowski et al., 2023

  • The correlation between SAM's segmentation performance and medical objects' attributes has not been conducted carefully.

    “Thus, the correlation between SAM's segmentation performance and medical objects' attributes has not been conducted carefully (He et al., 2023; Mazurowski et al., 2023; Ma and Wang, 2023).”

    From Segment anything model for medical images? (2024) · cites this paper as Mazurowski et al., 2023

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • Box-per-region strategy is assigned two mode numbers

    Minor

    The main text identifies a separate box for each object region as Mode 4, but the graphical abstract labels that strategy Mode 2.

  • Dataset count differs between the paper and graphical abstract

    Minor

    The paper states that it evaluates 19 datasets, while the graphical abstract says 18.

2 of 2

Cites

Flagged first, then by citations

Research works printed but not linked: 1

  1. Bradski, 2000, The OpenCV Library, Dr. Dobb’s J. Softw. Tools

Cited by

Sorted by citations

Authors
Mazurowski, M. A., Dong, H., Gu, H., Yang, J., Konz, N., & Zhang, Y.
Affiliations
Duke University (US)
Corresponding author
Dong, Haoyu
Venue
Medical Image Analysis
Publisher
Elsevier BV
Published
2023-10
Volume
89
Pages
102918
ISSN
1361-8415 (ISSN-L)
OpenAlex
W4385481295
Cited by
802
References
40
Citations by year
2026: 194 · 2025: 315 · 2024: 242 · 2023: 51
FWCI
72.49
Type
journal article
Language
en
Open access
Locations
  • Medical Image Analysis (acceptedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
  • arXiv (Cornell University) (submittedVersion, cc-by)
  • arXiv (Cornell University) (cc-by)
Funders
  • National Institutes of Health
  • National Heart, Lung, and Blood Institute (R44HL152825)
  • National Institute of Biomedical Imaging and Bioengineering (R01EB031575)
Topics
  • Physical Sciences › Computer Science › Computer Vision and Pattern Recognition › Medical Image Segmentation Techniques
  • Physical Sciences › Computer Science › Computer Vision and Pattern Recognition › Advanced Neural Network Applications
  • Physical Sciences › Computer Science › Artificial Intelligence › Domain Adaptation and Few-Shot Learning
Keywords
Segment Anything Model, medical image segmentation, zero-shot segmentation, interactive segmentation, point prompts, iterative segmentation, brain tumor segmentation, organ segmentation, medical imaging modalities, foundation models
MeSH terms
Brain Neoplasms, Humans, S-Adenosylmethionine, Tomography, X-Ray Computed

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